From d4505fe7ead8da6d4fdf7e0b4680f66b3a408e87 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:26:47 +0000
Subject: [PATCH] isGap method implemented in utils, and optimized

---
 src/jalview/schemes/PIDColourScheme.java     |    8 ++--
 src/jalview/schemes/ResidueColourScheme.java |   59 ++++++++------------------
 2 files changed, 20 insertions(+), 47 deletions(-)

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e587fee..cc050d5 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,7 +16,7 @@ public class PIDColourScheme extends ResidueColourScheme {
     }
 
 
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {
+  public Color findColour(String s, int j,Vector aa) {
       Color     c    = Color.white;
       Hashtable hash = null;
 
@@ -31,10 +31,9 @@ public class PIDColourScheme extends ResidueColourScheme {
       double sc = 0;
       if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))
       {
-
         sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;
         // MC Should be isGap
-        if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
+        if (!jalview.util.Comparison.isGap((s.charAt(0))))
         {
           for (int i = 0; i < thresholds.length; i++)
           {
@@ -45,8 +44,7 @@ public class PIDColourScheme extends ResidueColourScheme {
             }
           }
         }
-        else
-          c = Color.white;
+
       }
       return c;
   }
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f16bcca..b0a5caa 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -6,7 +6,7 @@ import java.awt.*;
 
 public class ResidueColourScheme implements ColourSchemeI{
     Color    [] colors;
-    int         threshold = 90;
+    int       threshold = 0;
 
     public ResidueColourScheme(Color[] colors, int threshold) {
 	this.colors    = colors;
@@ -21,31 +21,14 @@ public class ResidueColourScheme implements ColourSchemeI{
       return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
     }
 
-    public Color findColour(SequenceI seq,String s, int j, Vector aa) {
-  try {
-	    return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-	} catch (Exception e) {
-	    return Color.white;
-	}
-    }
-
-    // aa should maybe be a class
-  /*  public Color getColour(SequenceI seq, int j,Vector aa) {
-
-	Color  c       = Color.white;
-	String s       = seq.getSequence(j,j+1);
-
-	if (threshold > 0 && aa != null)
-        {
-	    if (aboveThreshold(aa,seq,j,threshold))
-		c = findColour(seq,s,j,aa);
-	}
-        else
-	    c = findColour(seq,s,j,aa);
+    public Color findColour(String s, int j, Vector aa) {
 
+       if( threshold==0 || aboveThreshold(aa,s,j))
+          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
+       else
+          return Color.white;
 
-      return c;
-    }*/
+    }
 
     public int getThreshold() {
 	return threshold;
@@ -55,29 +38,21 @@ public class ResidueColourScheme implements ColourSchemeI{
 	threshold = ct;
     }
 
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
-	String    s    = seq.getSequence(j,j+1);
-	Hashtable hash = (Hashtable)aa.elementAt(j);
+    public boolean aboveThreshold(Vector aa,String s, int j)
+    {
 
-	if (j < aa.size()) {
-	    String maxRes = (String)hash.get("maxResidue");
+	Hashtable hash = (Hashtable)aa.elementAt(j);
 
-	    double sc = 0;
+        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
+        {
+               ////  resCount////////////////////                  ///////////////seq count////////////
+          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();
 
-	    if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {
-		int maxCount = ((Integer)hash.get("maxCount")).intValue();
-		int resCount = ((Integer)hash.get(s)).intValue();
+          if (sc >= threshold)
+            return true;
 
-		sc = resCount * 100.0 / resCount;
+        }
 
-		// This should be isGap somewhere
-		if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {
-		    if (sc >= (double)threshold) {
-			return true;
-		    }
-		}
-	    }
-	}
 	return false;
     }
 
-- 
1.7.10.2